ITScorePro: An efficient scoring program for evaluating the energy scores of protein structures for structure prediction

Abstract

One important component in protein structure prediction is to evaluate the free energy of a given conformation. Given the enormous number of possible conformations for a sequence, it is extremely challenging to quickly and accurately score the energies of these conformations and predict a reasonable structure within a practical computational time. Here, we describe an efficient program for energy evaluation, referred to as ITScorePro (Copyright © 2012). The energy scoring function in the ITScorePro program is based on the distance-dependent, pairwise atomic potentials for protein structure prediction that we recently derived by using statistical mechanics principles (Huang and Zou, Proteins 79:2648– 2661, 2011). ITScorePro is a stand-alone program and can also be easily implemented in other software suites for protein structure prediction.